rpt.UAF {KinMixLite}

Replace CPTs in a DNA mixture to model uncertain allele frequencies

Description

Replace CPTs in a DNA mixture to model uncertainty in allele frequencies

Usage

replace.tables.for.UAF(mixture, M, compile = TRUE)

rpt.UAF(mixture, M, compile = TRUE)

Arguments

mixture

DNAmixtures object created by previous call to DNAmixture with
triangulate=FALSE,compile=FALSE

M

Size of allele frequency database

compile

logical flag: should mixture object be compiled on exit?

Value

No value is returned, the function is called for its side effect

Author(s)

Peter Green ([e-mail])

Examples

data(test2data)
data(NGMDyes)

## Fit 2-person mixture - baseline model

mixD<-DNAmixture(list(epg),k=2,C=list(0.001),database=db)
pars<-mixpar(rho=list(2),eta=list(100),xi=list(0.1),phi=list(c(U1=0.7,U2=0.3)))
baseline<-logL(mixD)(pars)

## Fit 2-person mixture model under assumption that database size was only 40

mixD<-DNAmixture(list(epg),k=2,C=list(0.001),database=db,triangulate=FALSE,compile=FALSE)
replace.tables.for.UAF(mixD,40)
log10LR<-(logL(mixD)(pars)-baseline)/log(10)
cat('log10 LR',log10LR,'\n')